variancePartition 1.1.7
Gabriel E. Hoffman
| Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/variancePartition | | Last Changed Rev: 112341 / Revision: 116626 | | Last Changed Date: 2016-01-08 09:57:10 -0800 (Fri, 08 Jan 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings variancePartition_1.1.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/variancePartition.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.1.7’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘variancePartition’ can be installed ... [7s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘variancePartition’ for: ‘residuals’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.fitExtractVarPartModel: no visible global function definition for ‘lm’
.fitVarPartModel: no visible global function definition for ‘lm’
.sortCols: no visible binding for global variable ‘median’
colinearityScore: no visible global function definition for ‘vcov’
colinearityScore: no visible global function definition for ‘cov2cor’
getVarianceComponents: no visible binding for global variable ‘var’
ggColorHue: no visible global function definition for ‘hcl’
plotStratifyBy: no visible global function definition for ‘reorder’
plotStratifyBy: no visible binding for global variable ‘median’
plotStratifyBy : <anonymous>: no visible global function definition for
‘median’
sortCols: no visible binding for global variable ‘median’
calcVarPart,lm: no visible global function definition for ‘anova’
checkModelStatus,lm: no visible global function definition for ‘coef’
checkModelStatus,lmerMod: no visible global function definition for
‘coef’
checkModelStatus,lmerMod: no visible global function definition for
‘terms’
residuals,VarParFitList : <anonymous>: no visible global function
definition for ‘residuals’
residuals,VarParFitList: no visible global function definition for
‘fitted.values’
sortCols,data.frame: no visible binding for global variable ‘median’
sortCols,matrix: no visible binding for global variable ‘median’
sortCols,varPartResults: no visible binding for global variable
‘median’
Undefined global functions or variables:
anova coef cov2cor fitted.values hcl lm median reorder residuals
terms var vcov
Consider adding
importFrom("grDevices", "hcl")
importFrom("stats", "anova", "coef", "cov2cor", "fitted.values", "lm",
"median", "reorder", "residuals", "terms", "var", "vcov")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [53s/138s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
fitVarPartModel-method 21.781 1.419 36.269
extractVarPart 12.145 0.673 23.413
getVarianceComponents 4.359 0.873 10.923
residuals-VarParFitList-method 3.077 0.334 9.387
fitExtractVarPartModel-method 1.207 0.084 22.123
plotPercentBars 0.819 0.044 10.298
plotVarPart-method 0.695 0.036 9.960
sortCols-method 0.685 0.033 10.048
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/variancePartition.Rcheck/00check.log’
for details.